Table 3.
Assembly summary statistics for de novo and hybrid assemblies.
| Organism | NGS technology | No. of contigs | Maximum contig size (kb) | N50 (kb) | Genome size (Mb) | Software |
|---|---|---|---|---|---|---|
| Clostridium thermocellum AD2 | Illumina | 102 | 331 | 116 | 3.48 | SPAdes* |
| 107 | 282 | 84 | 3.54 | ABySS | ||
| Illumina + PacBio | 14 | 2,270 | 2,270 | 3.57 | SPAdes | |
| PacBio-only | 10 | 982 | 891 | 3.49 | SMRTanalysis v 2.2 | |
| PacBio-only | 1 | 3,554 | 3,554 | 3.55 | Manual Finishing | |
| Halomonas sp. KO116 | Illumina | 110 | 373 | 194 | 5.13 | SPAdes* |
| 120 | 315 | 115 | 5.19 | ABySS | ||
| Illumina + PacBio | 30 | 4,654 | 4,654 | 5.19 | SPAdes | |
| PacBio-only | 1 (+ 2)a | 4,649 | 4,649 | 4.65 (+ 0.51)a | SMRTanalysis v 2.2 | |
| Pelosinus sp. UFO1 | Illumina | 175 | 1,025 | 637 | 5.13 | SPAdes |
| 131 | 169 | 78 | 5.03 | ABySS* | ||
| Illumina + PacBio | 147 | 4,498 | 4,498 | 5.19 | SPAdes | |
| PacBio-only | 1 | 5,115 | 5,115 | 5.12 | SMRTanalysis v 2.1b | |
| Pelosinus fermentans JBW45 | Illumina | 70 | 477 | 244 | 5.3 | SPAdes* |
| 114 | 318 | 110 | 5.4 | ABySS | ||
| Illumina + PacBio | 1 | 5,381 | 5,381 | 5.38 | SPAdes | |
| PacBio-only | 1 | 5,381 | 5,381 | 5.38 | SMRTanalysis v 2.2 | |
| Clostridium paradoxum JW-YL-7 | Illumina | 661 | 293 | 121 | 2.23 | SPAdes |
| 43 | 235 | 74 | 1.84 | ABySS* | ||
| Illumina + PacBio | 612 | 1,061 | 323 | 2.26 | SPAdes | |
| PacBio-only | 3 | 1,855 | 1,855 | 1.93 | SMRTanalysis v 2.2 | |
| Bacteroides cellulosolvens DSM 2933 | Illumina | 194 | 1,143 | 271 | 6.81 | SPAdes |
| 172 | 358 | 130 | 6.99 | ABySS* | ||
| Illumina + PacBio | 122 | 3,522 | 3,522 | 6.91 | SPAdes | |
| PacBio-only | 12 | 2,261 | 1,340 | 6.94 | SMRTanalysis v 2.0b | |
| PacBio-only | 3 | 6,349 | 6,349 | 6.88 | SMRTanalysis v 2.2 | |
| PacBio-only | 1 | 6,878 | 6,878 | 6.87 | Manual Finishing | |
| Clostridium pasteurianum ATCC 6013 | Illumina | 6 | 4,108 | 4,108 | 4.36 | SPAdes* |
| 101 | 207 | 73 | 4.35 | ABySS | ||
| Illumina + PacBio | 9 | 4,022 | 4,022 | 4.36 | SPAdes | |
| PacBio-only | 2 | 4,374 | 4,374 | 4.39 | SMRTanalysis v 2.2 |
Best assemblies shown in bold. The best draft assembly achieved with only the Illumina data are marked with *.
a
Additional numbers shown in brackets correspond to the extra-chromosomal plasmid DNA.
b
Assemblies performed prior to the availability of SMRTanalysis version 2.2. Prior assemblies are included to describe the effectiveness of algorithm improvement on genome assembly using the same data.